Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma
Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma
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DOI：
10.1038/s41379-019-0371-0
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发表时间：
2020-02-01
期刊：
影响因子：
7.5
通讯作者：
Pilotti, Silvana
中科院分区：
文献类型：
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作者：
Brich, Silvia;Bozzi, Fabio;Pilotti, Silvana
本研究的目的是评估荧光原位杂交 (FISH) 在鉴定三个关键腹膜间皮瘤肿瘤抑制基因 BAP1、CDKN2A 和 NF2 的拷贝数谱中的性能，特别强调微小纯合缺失，这是最近使用高通量方法在 3p21 (BAP1) 染色体区域发现的拷贝数异常。对 75 个福尔马林固定石蜡包埋的腹膜间皮瘤进行 FISH，发现两种类型的单等位基因缺失（单体性和半合子缺失）和两种类型的双等位基因缺失（FISH 信号完全缺失的典型纯合缺失和信号减弱的纯合缺失）。 FISH 信号减弱揭示了基因特异性探针覆盖的基因组区域内发生了缺失，并影响了所有三种肿瘤抑制因子。信号减弱的 BAP1 纯合缺失数量超过了典型纯合缺失（13 比 3）：相反，CDKN2A 普遍存在典型纯合缺失（2 比 14）。减少信号纯合缺失是 NF2 观察到的唯一双等位基因丢失模式（2 例）。半合子缺失主要影响 BAP1（21 比 6），而单体性在 CDKN2A 中普遍存在（14 比 7），尤其是 NF2，它是所有单等位基因丢失的原因。 FISH/免疫组织化学（BAP1、CDKN2A 和 MTAP）相关性表明，所有纯合缺失（包括信号减弱的缺失）都会导致 BAP1 和 CDKN2A 免疫表型无效，但只有典型的 CDKN2A 纯合缺失才会导致 MTAP 表达缺失。 BAP1 半合子缺失（而非单体性）也总是与蛋白质表达缺失相关，而 CDKN2A 单等位基因缺失类型均与 p16 或 MTAP 免疫组织化学相关。在自发出现的腹膜间皮瘤细胞系上进行的阵列比较基因组杂交为 FISH 模式的解释提供了支持，并使我们能够将间皮瘤中涉及的染色质重塑因子的数量扩展到 SETD7 和 PCGF5（两个以前未报告的基因）。
The aim of this study was to assess the performance of fluorescence in situ hybridization (FISH) in identifying the copy number profiles of the three key peritoneal mesothelioma tumor suppressor genes BAP1, CDKN2A, and NF2, with particular emphasis on minute homozygous deletions, a copy number abnormality recently unveiled at the 3p21 (BAP1) chromosomal region using high-throughput methods. FISH was performed on 75 formalin-fixed-paraffin-embedded peritoneal mesotheliomas and recognized two types of monoallelic loss (monosomy, and hemizygous deletion) and two types of biallelic loss (canonical homozygous deletion with a complete loss of FISH signal and homozygous deletion with diminished signal). Diminished FISH signals revealed deletions occurring within the genomic region covered by the gene-specific probe and affected all three tumor suppressors. BAP1 homozygous deletions with diminished signal outnumbered canonical homozygous deletions (13 vs 3): conversely, canonical homozygous deletions were prevalent for CDKN2A (2 vs 14). Diminished signal homozygous deletion was the only pattern of biallelic loss observed for NF2 (2 cases). Hemizygous deletion mainly affected BAP1 (21 vs 6), while monosomy was prevalent for CDKN2A (14 vs 7) and particularly for NF2 where it accounts for all monoallelic losses. FISH/immunohistochemistry (BAP1, CDKN2A, and MTAP) correlation showed that all homozygous deletions, including those with diminished signals, resulted in a null BAP1 and CDKN2A immunophenotype but only canonical CDKN2A homozygous deletions resulted in MTAP loss of expression. BAP1 hemizygous deletion, but not monosomy, was also invariably associated with loss of protein expression whereas neither type of CDKN2A monoallelic loss correlated with p16 or MTAP immunohistochemistry. Array comparative genomic hybridization performed on a spontaneously emerging peritoneal mesothelioma cell line provided support for the interpretation of the FISH patterns and allowed us to extend the number of chromatin remodeling factors involved in mesothelioma to SETD7 and PCGF5, two previously unreported genes.